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RGI/main export versions as explicit emission strings (#1909)

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* Export versions  as explicit emission strings in addition to versions.yml for compatibility with hAMRonization

* Update YML
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James A. Fellows Yates 2022-07-20 10:33:53 +02:00 committed by GitHub
parent 7e8ad56688
commit f91abed951
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2 changed files with 14 additions and 3 deletions
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9
modules/rgi/main/main.nf
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@ -13,6 +13,8 @@ process RGI_MAIN {
output: output:
tuple val(meta), path("*.json"), emit: json tuple val(meta), path("*.json"), emit: json
tuple val(meta), path("*.txt") , emit: tsv tuple val(meta), path("*.txt") , emit: tsv
env VER , emit: tool_version
env DBVER , emit: db_version
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -29,10 +31,13 @@ process RGI_MAIN {
--output_file $prefix \\ --output_file $prefix \\
--input_sequence $fasta --input_sequence $fasta
VER=\$(rgi main --version)
DBVER=\$(rgi database --version)
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
rgi: \$(rgi main --version) rgi: \$(echo \$VER)
rgi-database: \$(rgi database --version) rgi-database: \$(echo \$DBVER)
END_VERSIONS END_VERSIONS
""" """
} }

8
modules/rgi/main/meta.yml
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@ -42,6 +42,12 @@ output:
type: file type: file
description: Tab-delimited file with RGI results description: Tab-delimited file with RGI results
pattern: "*.{txt}" pattern: "*.{txt}"
- tool_version:
type: string
description: The version of the tool in string format (useful for downstream tools such as hAMRronization)
- db_version:
type: string
description: The version of the used database in string format (useful for downstream tools such as hAMRronization)
authors: authors:
- "@rpetit3" - "@rpetit3"
- "@jfy133"